I am interested in refining a DNA structure with phenix. However, as soon as I read my PDB, I get a warning for missing restraints: PHENIX could not find geometry restraints in the standard monomer library for one or more residues in the PDB file" what is the correct nomenclature for DNA and RNA for use in PHENIX?

phenix.refine should automatically recognize all commonly used DNA and RNA residue names. Do you have modified bases in your model?

Can I access phenix.elbow from the GUI ?

ReadySet under "Model tools" will run elbow if required. Ralf

For RNA I use ' Ar', ' Gr', ' Cr', ' Ur' (for the three letter field allotted) and sugar atoms have * as the last position of the three letter field allowed for atom defs. If you don't put these asterisks, coot doesn't recognize them and blows them into space upon real space refine ( to put it figuratively) F On Apr 30, 2010, at 9:23 AM, riya doreen wrote:

Hi Everyone,

I am interested in refining a DNA structure with phenix. However, as soon as I read my PDB, I get a warning for missing restraints: PHENIX could not find geometry restraints in the standard monomer library for one or more residues in the PDB file"

what is the correct nomenclature for DNA and RNA for use in PHENIX?

Can I access phenix.elbow from the GUI ?

Thanks _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D